[English] 日本語
Yorodumi
- PDB-7txw: Crystal structure of the complex of the malaria sexual stage prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7txw
TitleCrystal structure of the complex of the malaria sexual stage protein and vaccine target Pfs25 with the Fab fragment of a transmission blocking antibody 1G2
Components
  • (Fab fragment of monoclonal antibody 1G2 ...) x 2
  • Ookinete surface protein P25
KeywordsIMMUNE SYSTEM / malaria / transmission blocking vaccine
Function / homology
Function and homology information


cell surface / plasma membrane
Similarity search - Function
Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / Epidermal growth factor-like domain. / EGF-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHANOL / DI(HYDROXYETHYL)ETHER / Ookinete surface protein P25
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsSingh, K. / Gittis, A.G. / Garboczi, D.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Npj Vaccines / Year: 2023
Title: Structural and immunological differences in Plasmodium falciparum sexual stage transmission-blocking vaccines comprised of Pfs25-EPA nanoparticles.
Authors: MacDonald, N.J. / Singh, K. / Reiter, K. / Nguyen, V. / Shimp Jr., R. / Gittis, A.G. / Chen, B. / Burkhardt, M. / Zhang, B. / Wang, Z. / Herrera, R. / Moler, M. / Lee, D.Y. / Orr-Gonzalez, S. ...Authors: MacDonald, N.J. / Singh, K. / Reiter, K. / Nguyen, V. / Shimp Jr., R. / Gittis, A.G. / Chen, B. / Burkhardt, M. / Zhang, B. / Wang, Z. / Herrera, R. / Moler, M. / Lee, D.Y. / Orr-Gonzalez, S. / Herrod, J. / Lambert, L.E. / Rausch, K.M. / Muratova, O. / Jones, D.S. / Wu, Y. / Jin, A.J. / Garboczi, D.N. / Duffy, P.E. / Narum, D.L.
History
DepositionFeb 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab fragment of monoclonal antibody 1G2 light chain
H: Fab fragment of monoclonal antibody 1G2 heavy chain
A: Ookinete surface protein P25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,59620
Polymers66,4133
Non-polymers1,18317
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.320, 50.170, 100.030
Angle α, β, γ (deg.)90.000, 123.096, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules A

#3: Protein Ookinete surface protein P25


Mass: 18716.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1031000 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q7KQL2

-
Antibody , 2 types, 2 molecules LH

#1: Antibody Fab fragment of monoclonal antibody 1G2 light chain


Mass: 24226.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HEK293 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Fab fragment of monoclonal antibody 1G2 heavy chain


Mass: 23469.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Non-polymers , 5 types, 273 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 20-25% PEG 6000, 0.1 M HEPES, pH 7.5 and cocktail of low molecular alcohols as additives

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→60.97 Å / Num. obs: 26678 / % possible obs: 98.3 % / Redundancy: 4.92 % / Biso Wilson estimate: 23.32 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.62
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.22 / Num. unique obs: 1649 / CC1/2: 0.882 / % possible all: 83.6

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house Fab models

Resolution: 2.17→60.97 Å / SU ML: 0.225 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.9136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 1811 6.99 %
Rwork0.1767 24115 -
obs0.1804 25926 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.69 Å2
Refinement stepCycle: LAST / Resolution: 2.17→60.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 77 256 4228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924045
X-RAY DIFFRACTIONf_angle_d1.1975477
X-RAY DIFFRACTIONf_chiral_restr0.0678621
X-RAY DIFFRACTIONf_plane_restr0.008692
X-RAY DIFFRACTIONf_dihedral_angle_d16.70091429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.2698990.19231469X-RAY DIFFRACTION76.98
2.23-2.30.28321460.19021800X-RAY DIFFRACTION93.24
2.3-2.370.23841420.19431834X-RAY DIFFRACTION94.86
2.37-2.460.27821300.2031817X-RAY DIFFRACTION95.91
2.46-2.560.29981430.19991848X-RAY DIFFRACTION95.54
2.56-2.670.27271420.1991858X-RAY DIFFRACTION96.95
2.67-2.810.24381400.19771884X-RAY DIFFRACTION97.83
2.81-2.990.23681390.19231890X-RAY DIFFRACTION97.92
2.99-3.220.27461410.17811917X-RAY DIFFRACTION98.85
3.22-3.540.20711470.16931904X-RAY DIFFRACTION99.32
3.54-4.060.20551400.15691949X-RAY DIFFRACTION99.57
4.06-5.110.171500.13971961X-RAY DIFFRACTION99.34
5.11-60.970.21511520.18731984X-RAY DIFFRACTION98.75

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more